Rotational Effects within Nucleosome Core Particles on Abasic Site Reactivity

Area of Science:

• Biochemistry
• Molecular Biology
• Genetics

Background:

• Abasic (AP) sites are frequent DNA lesions arising from various cellular processes.
• These lesions are cytotoxic and mutagenic, necessitating cellular protection via DNA repair pathways like base excision repair (BER).
• AP sites are alkali-labile, with a long half-life for strand scission in free DNA, but are destabilized within nucleosome core particles (NCPs).

Purpose of the Study:

• To investigate the influence of rotational positioning within NCPs on the rate of strand scission at AP sites.
• To understand how histone proteins affect the reactivity and repair of AP sites.
• To elucidate the structural basis for the interaction between histone proteins and AP sites.

Main Methods:

• Experimental examination of strand scission rates at AP sites across varying rotational positions within NCPs.
• Analysis of reactivity changes over approximately one helical turn of DNA.
• Molecular modeling based on NCP X-ray crystal structures to visualize histone-DNA interactions.

Main Results:

• The rate constant for strand scission at AP sites within NCPs varied only ~4-fold with rotational position, a significantly smaller range than observed for reactions with diffusible reagents.
• No obvious pattern in the rate constant change was detected concerning rotational position.
• Molecular modeling suggests histone protein tails can access AP sites through either the major or minor groove.

Conclusions:

• Histone protein interactions significantly dampen the effect of rotational positioning on AP site strand scission reactivity within NCPs.
• The accessibility of AP sites to histone tails via both grooves explains the limited positional dependence.
• Further research is needed to delineate the roles of individual histone proteins and the precise chemical mechanism involving Schiff base formation.